Multiple sequence alignment - TraesCS3B01G073600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G073600 chr3B 100.000 4401 0 0 658 5058 44279164 44283564 0.000000e+00 8128
1 TraesCS3B01G073600 chr3B 100.000 400 0 0 1 400 44278507 44278906 0.000000e+00 739
2 TraesCS3B01G073600 chr3B 88.089 403 26 5 1 400 38815524 38815141 4.610000e-125 459
3 TraesCS3B01G073600 chr3B 88.089 403 26 5 1 400 38831855 38831472 4.610000e-125 459
4 TraesCS3B01G073600 chr3B 83.863 409 36 12 1 400 603308780 603308393 3.720000e-96 363
5 TraesCS3B01G073600 chr3B 94.340 106 6 0 658 763 38815113 38815008 4.050000e-36 163
6 TraesCS3B01G073600 chr3B 94.340 106 6 0 658 763 38831444 38831339 4.050000e-36 163
7 TraesCS3B01G073600 chr3B 79.121 273 27 12 3 260 127607524 127607781 1.460000e-35 161
8 TraesCS3B01G073600 chr3A 95.096 3630 125 32 1435 5058 36488620 36492202 0.000000e+00 5668
9 TraesCS3B01G073600 chr3A 88.323 471 22 8 918 1383 36488163 36488605 7.450000e-148 534
10 TraesCS3B01G073600 chr3A 83.764 271 17 11 755 998 36477952 36478222 1.100000e-56 231
11 TraesCS3B01G073600 chr3D 95.092 2282 69 17 2791 5058 26452681 26454933 0.000000e+00 3554
12 TraesCS3B01G073600 chr3D 91.174 1133 84 11 958 2083 26449204 26450327 0.000000e+00 1524
13 TraesCS3B01G073600 chr3D 90.145 690 45 10 2116 2802 26450394 26451063 0.000000e+00 876
14 TraesCS3B01G073600 chr3D 82.642 265 29 11 1935 2197 600659122 600659371 8.530000e-53 219
15 TraesCS3B01G073600 chr5B 93.500 400 25 1 1 400 685314830 685314432 1.210000e-165 593
16 TraesCS3B01G073600 chr4B 92.365 406 24 2 1 400 562422042 562421638 5.680000e-159 571
17 TraesCS3B01G073600 chr4B 92.308 403 27 2 1 400 590049751 590049350 2.040000e-158 569
18 TraesCS3B01G073600 chr4B 95.238 105 5 0 658 762 26018254 26018358 3.130000e-37 167
19 TraesCS3B01G073600 chr4B 95.238 105 5 0 658 762 26155627 26155731 3.130000e-37 167
20 TraesCS3B01G073600 chr4B 94.286 105 6 0 658 762 25980390 25980494 1.460000e-35 161
21 TraesCS3B01G073600 chr4B 94.286 105 6 0 658 762 26239351 26239455 1.460000e-35 161
22 TraesCS3B01G073600 chr4B 94.286 105 6 0 658 762 26278835 26278939 1.460000e-35 161
23 TraesCS3B01G073600 chr4B 95.098 102 5 0 658 759 655096737 655096838 1.460000e-35 161
24 TraesCS3B01G073600 chr6B 91.500 400 34 0 1 400 23448155 23448554 7.400000e-153 551
25 TraesCS3B01G073600 chr2B 91.500 400 25 1 1 400 17588020 17588410 4.450000e-150 542
26 TraesCS3B01G073600 chr2B 88.889 396 35 3 5 400 643430976 643431362 3.540000e-131 479
27 TraesCS3B01G073600 chr2B 80.303 264 35 12 1935 2197 560436799 560437046 3.110000e-42 183
28 TraesCS3B01G073600 chr1B 90.055 362 24 2 42 400 656615664 656615312 4.610000e-125 459
29 TraesCS3B01G073600 chr1B 95.098 102 5 0 658 759 480984971 480984870 1.460000e-35 161
30 TraesCS3B01G073600 chr4D 82.642 265 29 11 1935 2197 71380061 71379812 8.530000e-53 219
31 TraesCS3B01G073600 chr5A 81.273 267 27 15 1935 2197 181419415 181419168 1.440000e-45 195


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G073600 chr3B 44278507 44283564 5057 False 4433.500000 8128 100.0000 1 5058 2 chr3B.!!$F2 5057
1 TraesCS3B01G073600 chr3B 38815008 38815524 516 True 311.000000 459 91.2145 1 763 2 chr3B.!!$R2 762
2 TraesCS3B01G073600 chr3B 38831339 38831855 516 True 311.000000 459 91.2145 1 763 2 chr3B.!!$R3 762
3 TraesCS3B01G073600 chr3A 36488163 36492202 4039 False 3101.000000 5668 91.7095 918 5058 2 chr3A.!!$F2 4140
4 TraesCS3B01G073600 chr3D 26449204 26454933 5729 False 1984.666667 3554 92.1370 958 5058 3 chr3D.!!$F2 4100

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
833 837 0.035317 TTCATTGTCGCACCAGAGCT 59.965 50.0 0.00 0.00 0.0 4.09 F
1627 1660 0.095935 CGTTTGAGCTCCTGAATGCG 59.904 55.0 12.15 3.69 0.0 4.73 F
1631 1664 0.321346 TGAGCTCCTGAATGCGTTGA 59.679 50.0 12.15 0.00 0.0 3.18 F
3173 4879 0.324943 ATATATGTCCTGGTGCGGGC 59.675 55.0 0.00 0.00 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1789 1822 0.940126 AGGCTGCAAAGCGATAATCG 59.060 50.0 0.50 0.0 43.89 3.34 R
3384 5090 2.431057 AGGATAGTTGCTAAGGTCCACG 59.569 50.0 0.00 0.0 0.00 4.94 R
3488 5194 5.958955 AGCATCAGAAAATTGGAAGCTAAC 58.041 37.5 0.00 0.0 0.00 2.34 R
4890 6601 0.326522 TCCAGGCTGCCCTCAAGATA 60.327 55.0 16.57 0.0 40.33 1.98 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 4.802051 GATGAGGCGGCCAAGGCA 62.802 66.667 23.09 13.56 44.11 4.75
48 49 3.142838 GGCGCATGTTGGCCTCAT 61.143 61.111 10.83 6.22 45.93 2.90
70 71 4.821589 GACCAGCTTCCCTCGGCG 62.822 72.222 0.00 0.00 0.00 6.46
72 73 3.854669 CCAGCTTCCCTCGGCGAT 61.855 66.667 11.27 0.00 0.00 4.58
73 74 2.587194 CAGCTTCCCTCGGCGATG 60.587 66.667 11.27 7.82 0.00 3.84
74 75 3.077556 AGCTTCCCTCGGCGATGT 61.078 61.111 11.27 0.00 0.00 3.06
75 76 2.125106 GCTTCCCTCGGCGATGTT 60.125 61.111 11.27 0.00 0.00 2.71
76 77 2.464459 GCTTCCCTCGGCGATGTTG 61.464 63.158 11.27 0.00 0.00 3.33
77 78 2.435938 TTCCCTCGGCGATGTTGC 60.436 61.111 11.27 0.00 0.00 4.17
159 160 2.315781 GATGATGCCGAGACTGCCCA 62.316 60.000 0.00 0.00 0.00 5.36
201 202 4.767255 CACAGAGCACGAGGCCCC 62.767 72.222 0.00 0.00 46.50 5.80
290 291 2.048127 GGTGTCGAGACTGCCCAC 60.048 66.667 12.92 2.05 0.00 4.61
351 355 2.628106 CGCTTGATCGCCGGATTG 59.372 61.111 5.05 0.00 31.51 2.67
366 370 5.766150 CCGGATTGTGGCATCTATTTTAA 57.234 39.130 0.00 0.00 0.00 1.52
367 371 6.142818 CCGGATTGTGGCATCTATTTTAAA 57.857 37.500 0.00 0.00 0.00 1.52
372 376 3.685272 TGTGGCATCTATTTTAAACGCGA 59.315 39.130 15.93 0.00 0.00 5.87
377 381 5.446741 GGCATCTATTTTAAACGCGAGAACA 60.447 40.000 15.93 0.00 0.00 3.18
729 733 2.561373 CGGTTTTTCTGCGCCCTC 59.439 61.111 4.18 0.00 0.00 4.30
756 760 0.747255 GAACGGCTGGAGATGCTCTA 59.253 55.000 0.00 0.00 0.00 2.43
760 764 1.410517 CGGCTGGAGATGCTCTAAGAA 59.589 52.381 0.00 0.00 0.00 2.52
763 767 2.102925 GCTGGAGATGCTCTAAGAAGCT 59.897 50.000 0.00 0.00 42.94 3.74
764 768 3.799917 GCTGGAGATGCTCTAAGAAGCTC 60.800 52.174 0.00 0.00 42.94 4.09
765 769 3.638160 CTGGAGATGCTCTAAGAAGCTCT 59.362 47.826 0.56 0.00 42.94 4.09
766 770 3.636300 TGGAGATGCTCTAAGAAGCTCTC 59.364 47.826 12.74 12.74 42.94 3.20
767 771 3.005791 GGAGATGCTCTAAGAAGCTCTCC 59.994 52.174 19.23 19.23 46.79 3.71
768 772 3.891366 GAGATGCTCTAAGAAGCTCTCCT 59.109 47.826 11.19 0.00 42.94 3.69
769 773 3.891366 AGATGCTCTAAGAAGCTCTCCTC 59.109 47.826 0.00 0.00 42.94 3.71
770 774 2.020720 TGCTCTAAGAAGCTCTCCTCG 58.979 52.381 0.00 0.00 42.94 4.63
771 775 2.294074 GCTCTAAGAAGCTCTCCTCGA 58.706 52.381 0.00 0.00 39.27 4.04
772 776 2.032924 GCTCTAAGAAGCTCTCCTCGAC 59.967 54.545 0.00 0.00 39.27 4.20
773 777 2.281517 TCTAAGAAGCTCTCCTCGACG 58.718 52.381 0.00 0.00 0.00 5.12
774 778 2.093606 TCTAAGAAGCTCTCCTCGACGA 60.094 50.000 0.00 0.00 0.00 4.20
775 779 1.757682 AAGAAGCTCTCCTCGACGAT 58.242 50.000 0.00 0.00 0.00 3.73
776 780 1.021202 AGAAGCTCTCCTCGACGATG 58.979 55.000 0.00 0.00 0.00 3.84
777 781 1.018148 GAAGCTCTCCTCGACGATGA 58.982 55.000 0.00 0.00 0.00 2.92
778 782 1.606668 GAAGCTCTCCTCGACGATGAT 59.393 52.381 0.00 0.00 0.00 2.45
779 783 1.234821 AGCTCTCCTCGACGATGATC 58.765 55.000 0.00 0.00 0.00 2.92
780 784 0.947960 GCTCTCCTCGACGATGATCA 59.052 55.000 0.00 0.00 0.00 2.92
781 785 1.335182 GCTCTCCTCGACGATGATCAA 59.665 52.381 0.00 0.00 0.00 2.57
782 786 2.604373 GCTCTCCTCGACGATGATCAAG 60.604 54.545 0.00 0.00 0.00 3.02
783 787 1.335182 TCTCCTCGACGATGATCAAGC 59.665 52.381 0.00 0.00 0.00 4.01
784 788 1.066152 CTCCTCGACGATGATCAAGCA 59.934 52.381 0.00 0.00 0.00 3.91
785 789 1.066152 TCCTCGACGATGATCAAGCAG 59.934 52.381 0.00 0.00 0.00 4.24
786 790 1.485397 CTCGACGATGATCAAGCAGG 58.515 55.000 0.00 0.00 0.00 4.85
787 791 0.528466 TCGACGATGATCAAGCAGGC 60.528 55.000 0.00 0.00 0.00 4.85
788 792 1.815212 CGACGATGATCAAGCAGGCG 61.815 60.000 0.00 1.45 0.00 5.52
789 793 2.098842 GACGATGATCAAGCAGGCGC 62.099 60.000 0.00 0.00 38.99 6.53
790 794 2.175621 CGATGATCAAGCAGGCGCA 61.176 57.895 10.83 0.00 42.27 6.09
791 795 1.504647 CGATGATCAAGCAGGCGCAT 61.505 55.000 10.83 0.00 42.27 4.73
792 796 0.040336 GATGATCAAGCAGGCGCATG 60.040 55.000 19.36 19.36 42.27 4.06
793 797 2.025727 GATCAAGCAGGCGCATGC 59.974 61.111 37.46 37.46 46.88 4.06
799 803 3.829044 GCAGGCGCATGCAATCCA 61.829 61.111 38.85 0.00 45.77 3.41
800 804 2.886610 CAGGCGCATGCAATCCAA 59.113 55.556 19.57 0.00 45.35 3.53
801 805 1.226859 CAGGCGCATGCAATCCAAG 60.227 57.895 19.57 8.32 45.35 3.61
802 806 1.378911 AGGCGCATGCAATCCAAGA 60.379 52.632 19.57 0.00 45.35 3.02
803 807 1.065273 GGCGCATGCAATCCAAGAG 59.935 57.895 19.57 0.00 45.35 2.85
804 808 1.588139 GCGCATGCAATCCAAGAGC 60.588 57.895 19.57 5.54 42.15 4.09
805 809 1.804598 CGCATGCAATCCAAGAGCA 59.195 52.632 19.57 0.00 43.14 4.26
810 814 2.203470 TGCAATCCAAGAGCATGACA 57.797 45.000 0.00 0.00 32.55 3.58
811 815 1.814394 TGCAATCCAAGAGCATGACAC 59.186 47.619 0.00 0.00 32.55 3.67
812 816 1.133790 GCAATCCAAGAGCATGACACC 59.866 52.381 0.00 0.00 0.00 4.16
813 817 2.719739 CAATCCAAGAGCATGACACCT 58.280 47.619 0.00 0.00 0.00 4.00
814 818 3.087031 CAATCCAAGAGCATGACACCTT 58.913 45.455 0.00 0.00 0.00 3.50
815 819 2.957402 TCCAAGAGCATGACACCTTT 57.043 45.000 0.00 0.00 0.00 3.11
816 820 2.783135 TCCAAGAGCATGACACCTTTC 58.217 47.619 0.00 0.00 0.00 2.62
817 821 2.106338 TCCAAGAGCATGACACCTTTCA 59.894 45.455 0.00 0.00 0.00 2.69
818 822 3.087031 CCAAGAGCATGACACCTTTCAT 58.913 45.455 0.00 0.00 36.62 2.57
819 823 3.508793 CCAAGAGCATGACACCTTTCATT 59.491 43.478 0.00 0.00 33.74 2.57
820 824 4.482386 CAAGAGCATGACACCTTTCATTG 58.518 43.478 0.00 0.00 33.74 2.82
821 825 3.759581 AGAGCATGACACCTTTCATTGT 58.240 40.909 0.00 0.00 33.74 2.71
822 826 3.755378 AGAGCATGACACCTTTCATTGTC 59.245 43.478 0.00 0.00 42.18 3.18
823 827 2.485426 AGCATGACACCTTTCATTGTCG 59.515 45.455 0.00 0.00 44.35 4.35
824 828 2.855180 CATGACACCTTTCATTGTCGC 58.145 47.619 0.00 0.00 44.35 5.19
825 829 1.960417 TGACACCTTTCATTGTCGCA 58.040 45.000 0.00 0.00 44.35 5.10
826 830 1.601903 TGACACCTTTCATTGTCGCAC 59.398 47.619 0.00 0.00 44.35 5.34
827 831 0.951558 ACACCTTTCATTGTCGCACC 59.048 50.000 0.00 0.00 0.00 5.01
828 832 0.950836 CACCTTTCATTGTCGCACCA 59.049 50.000 0.00 0.00 0.00 4.17
829 833 1.069022 CACCTTTCATTGTCGCACCAG 60.069 52.381 0.00 0.00 0.00 4.00
830 834 1.202758 ACCTTTCATTGTCGCACCAGA 60.203 47.619 0.00 0.00 0.00 3.86
831 835 1.466167 CCTTTCATTGTCGCACCAGAG 59.534 52.381 0.00 0.00 0.00 3.35
832 836 0.874390 TTTCATTGTCGCACCAGAGC 59.126 50.000 0.00 0.00 0.00 4.09
833 837 0.035317 TTCATTGTCGCACCAGAGCT 59.965 50.000 0.00 0.00 0.00 4.09
834 838 0.390340 TCATTGTCGCACCAGAGCTC 60.390 55.000 5.27 5.27 0.00 4.09
835 839 1.078848 ATTGTCGCACCAGAGCTCC 60.079 57.895 10.93 0.00 0.00 4.70
836 840 2.527951 ATTGTCGCACCAGAGCTCCC 62.528 60.000 10.93 0.00 0.00 4.30
837 841 3.695606 GTCGCACCAGAGCTCCCA 61.696 66.667 10.93 0.00 0.00 4.37
838 842 2.685017 TCGCACCAGAGCTCCCAT 60.685 61.111 10.93 0.00 0.00 4.00
839 843 2.202987 CGCACCAGAGCTCCCATC 60.203 66.667 10.93 0.00 0.00 3.51
840 844 2.993008 GCACCAGAGCTCCCATCA 59.007 61.111 10.93 0.00 0.00 3.07
841 845 1.300963 GCACCAGAGCTCCCATCAA 59.699 57.895 10.93 0.00 0.00 2.57
842 846 0.747283 GCACCAGAGCTCCCATCAAG 60.747 60.000 10.93 0.00 0.00 3.02
843 847 0.107312 CACCAGAGCTCCCATCAAGG 60.107 60.000 10.93 3.99 37.03 3.61
844 848 1.153005 CCAGAGCTCCCATCAAGGC 60.153 63.158 10.93 0.00 35.39 4.35
845 849 1.153005 CAGAGCTCCCATCAAGGCC 60.153 63.158 10.93 0.00 35.39 5.19
846 850 1.617536 AGAGCTCCCATCAAGGCCA 60.618 57.895 10.93 0.00 35.39 5.36
847 851 1.153005 GAGCTCCCATCAAGGCCAG 60.153 63.158 5.01 0.00 35.39 4.85
848 852 2.123982 GCTCCCATCAAGGCCAGG 60.124 66.667 5.01 0.00 35.39 4.45
849 853 2.683465 GCTCCCATCAAGGCCAGGA 61.683 63.158 5.01 1.12 35.39 3.86
850 854 1.225704 CTCCCATCAAGGCCAGGAC 59.774 63.158 5.01 0.00 35.39 3.85
851 855 1.541118 TCCCATCAAGGCCAGGACA 60.541 57.895 5.01 0.00 35.39 4.02
852 856 1.379044 CCCATCAAGGCCAGGACAC 60.379 63.158 5.01 0.00 35.39 3.67
853 857 1.379916 CCATCAAGGCCAGGACACA 59.620 57.895 5.01 0.00 0.00 3.72
854 858 0.962356 CCATCAAGGCCAGGACACAC 60.962 60.000 5.01 0.00 0.00 3.82
855 859 0.250858 CATCAAGGCCAGGACACACA 60.251 55.000 5.01 0.00 0.00 3.72
856 860 0.478072 ATCAAGGCCAGGACACACAA 59.522 50.000 5.01 0.00 0.00 3.33
857 861 0.257328 TCAAGGCCAGGACACACAAA 59.743 50.000 5.01 0.00 0.00 2.83
858 862 1.133513 TCAAGGCCAGGACACACAAAT 60.134 47.619 5.01 0.00 0.00 2.32
859 863 1.688197 CAAGGCCAGGACACACAAATT 59.312 47.619 5.01 0.00 0.00 1.82
860 864 1.620822 AGGCCAGGACACACAAATTC 58.379 50.000 5.01 0.00 0.00 2.17
861 865 1.133513 AGGCCAGGACACACAAATTCA 60.134 47.619 5.01 0.00 0.00 2.57
862 866 1.895131 GGCCAGGACACACAAATTCAT 59.105 47.619 0.00 0.00 0.00 2.57
863 867 2.299867 GGCCAGGACACACAAATTCATT 59.700 45.455 0.00 0.00 0.00 2.57
864 868 3.319755 GCCAGGACACACAAATTCATTG 58.680 45.455 0.00 0.00 44.95 2.82
865 869 3.319755 CCAGGACACACAAATTCATTGC 58.680 45.455 0.00 0.00 43.13 3.56
866 870 3.243805 CCAGGACACACAAATTCATTGCA 60.244 43.478 0.00 0.00 43.13 4.08
867 871 4.370049 CAGGACACACAAATTCATTGCAA 58.630 39.130 0.00 0.00 43.13 4.08
868 872 4.809958 CAGGACACACAAATTCATTGCAAA 59.190 37.500 1.71 0.00 43.13 3.68
869 873 5.293814 CAGGACACACAAATTCATTGCAAAA 59.706 36.000 1.71 0.00 43.13 2.44
870 874 5.524646 AGGACACACAAATTCATTGCAAAAG 59.475 36.000 1.71 0.00 43.13 2.27
871 875 5.523188 GGACACACAAATTCATTGCAAAAGA 59.477 36.000 1.71 1.42 43.13 2.52
872 876 6.036953 GGACACACAAATTCATTGCAAAAGAA 59.963 34.615 16.82 16.82 43.13 2.52
873 877 7.375106 ACACACAAATTCATTGCAAAAGAAA 57.625 28.000 17.97 5.47 43.13 2.52
874 878 7.987649 ACACACAAATTCATTGCAAAAGAAAT 58.012 26.923 17.97 9.83 43.13 2.17
875 879 8.124199 ACACACAAATTCATTGCAAAAGAAATC 58.876 29.630 17.97 0.00 43.13 2.17
876 880 8.123575 CACACAAATTCATTGCAAAAGAAATCA 58.876 29.630 17.97 0.63 43.13 2.57
877 881 8.842280 ACACAAATTCATTGCAAAAGAAATCAT 58.158 25.926 17.97 3.33 43.13 2.45
883 887 8.721019 TTCATTGCAAAAGAAATCATATTCCC 57.279 30.769 1.71 0.00 29.65 3.97
884 888 8.081517 TCATTGCAAAAGAAATCATATTCCCT 57.918 30.769 1.71 0.00 0.00 4.20
885 889 7.982919 TCATTGCAAAAGAAATCATATTCCCTG 59.017 33.333 1.71 0.00 0.00 4.45
886 890 7.479352 TTGCAAAAGAAATCATATTCCCTGA 57.521 32.000 0.00 0.00 0.00 3.86
887 891 7.479352 TGCAAAAGAAATCATATTCCCTGAA 57.521 32.000 0.00 0.00 0.00 3.02
888 892 7.905265 TGCAAAAGAAATCATATTCCCTGAAA 58.095 30.769 0.00 0.00 0.00 2.69
889 893 8.373981 TGCAAAAGAAATCATATTCCCTGAAAA 58.626 29.630 0.00 0.00 0.00 2.29
890 894 9.218440 GCAAAAGAAATCATATTCCCTGAAAAA 57.782 29.630 0.00 0.00 0.00 1.94
893 897 8.953368 AAGAAATCATATTCCCTGAAAAATGC 57.047 30.769 0.00 0.00 0.00 3.56
894 898 8.081517 AGAAATCATATTCCCTGAAAAATGCA 57.918 30.769 0.00 0.00 0.00 3.96
895 899 8.542080 AGAAATCATATTCCCTGAAAAATGCAA 58.458 29.630 0.00 0.00 0.00 4.08
896 900 9.165035 GAAATCATATTCCCTGAAAAATGCAAA 57.835 29.630 0.00 0.00 0.00 3.68
897 901 9.517868 AAATCATATTCCCTGAAAAATGCAAAA 57.482 25.926 0.00 0.00 0.00 2.44
898 902 8.726870 ATCATATTCCCTGAAAAATGCAAAAG 57.273 30.769 0.00 0.00 0.00 2.27
899 903 7.678837 TCATATTCCCTGAAAAATGCAAAAGT 58.321 30.769 0.00 0.00 0.00 2.66
900 904 7.603404 TCATATTCCCTGAAAAATGCAAAAGTG 59.397 33.333 0.00 0.00 0.00 3.16
901 905 5.350504 TTCCCTGAAAAATGCAAAAGTGA 57.649 34.783 0.00 0.00 0.00 3.41
902 906 5.549742 TCCCTGAAAAATGCAAAAGTGAT 57.450 34.783 0.00 0.00 0.00 3.06
903 907 5.540911 TCCCTGAAAAATGCAAAAGTGATC 58.459 37.500 0.00 0.00 0.00 2.92
904 908 5.070180 TCCCTGAAAAATGCAAAAGTGATCA 59.930 36.000 0.00 0.00 0.00 2.92
905 909 5.759273 CCCTGAAAAATGCAAAAGTGATCAA 59.241 36.000 0.00 0.00 0.00 2.57
906 910 6.260493 CCCTGAAAAATGCAAAAGTGATCAAA 59.740 34.615 0.00 0.00 0.00 2.69
907 911 7.040961 CCCTGAAAAATGCAAAAGTGATCAAAT 60.041 33.333 0.00 0.00 0.00 2.32
908 912 8.013378 CCTGAAAAATGCAAAAGTGATCAAATC 58.987 33.333 0.00 0.00 0.00 2.17
909 913 7.565848 TGAAAAATGCAAAAGTGATCAAATCG 58.434 30.769 0.00 0.00 0.00 3.34
910 914 6.470557 AAAATGCAAAAGTGATCAAATCGG 57.529 33.333 0.00 0.00 0.00 4.18
911 915 4.789012 ATGCAAAAGTGATCAAATCGGT 57.211 36.364 0.00 0.00 0.00 4.69
912 916 5.895636 ATGCAAAAGTGATCAAATCGGTA 57.104 34.783 0.00 0.00 0.00 4.02
913 917 5.697473 TGCAAAAGTGATCAAATCGGTAA 57.303 34.783 0.00 0.00 0.00 2.85
914 918 5.457140 TGCAAAAGTGATCAAATCGGTAAC 58.543 37.500 0.00 0.00 0.00 2.50
915 919 5.009110 TGCAAAAGTGATCAAATCGGTAACA 59.991 36.000 0.00 0.00 0.00 2.41
916 920 6.092748 GCAAAAGTGATCAAATCGGTAACAT 58.907 36.000 0.00 0.00 0.00 2.71
919 923 8.977505 CAAAAGTGATCAAATCGGTAACATTTT 58.022 29.630 0.00 0.00 0.00 1.82
964 968 2.678336 GACAAATCTGTCCCCATCGTTC 59.322 50.000 0.00 0.00 45.41 3.95
1100 1110 4.101448 CCACCCCTTCCTCGCAGG 62.101 72.222 0.00 0.00 36.46 4.85
1136 1167 4.439901 GCCCTCCCTCCCTCCCTT 62.440 72.222 0.00 0.00 0.00 3.95
1137 1168 2.367512 CCCTCCCTCCCTCCCTTG 60.368 72.222 0.00 0.00 0.00 3.61
1138 1169 3.093172 CCTCCCTCCCTCCCTTGC 61.093 72.222 0.00 0.00 0.00 4.01
1139 1170 3.093172 CTCCCTCCCTCCCTTGCC 61.093 72.222 0.00 0.00 0.00 4.52
1140 1171 4.760220 TCCCTCCCTCCCTTGCCC 62.760 72.222 0.00 0.00 0.00 5.36
1156 1187 3.585247 CCCCCTCCCATCTCCATG 58.415 66.667 0.00 0.00 0.00 3.66
1262 1293 2.284798 ATCCAGCGCGTGTCGAATCT 62.285 55.000 8.43 0.00 41.67 2.40
1270 1301 2.386249 GCGTGTCGAATCTAGATCACC 58.614 52.381 5.51 1.32 0.00 4.02
1274 1305 4.363999 GTGTCGAATCTAGATCACCCTTG 58.636 47.826 5.51 0.00 0.00 3.61
1277 1308 2.965831 CGAATCTAGATCACCCTTGGGA 59.034 50.000 13.39 0.00 0.00 4.37
1278 1309 3.580458 CGAATCTAGATCACCCTTGGGAT 59.420 47.826 13.39 0.00 0.00 3.85
1289 1320 0.179018 CCTTGGGATTGGACCGGATC 60.179 60.000 9.46 0.00 0.00 3.36
1356 1389 1.674441 TGTATCCTTCTGACCGCGTAG 59.326 52.381 4.92 0.01 0.00 3.51
1383 1416 3.460648 GCTGTAATTCGGCCACTCT 57.539 52.632 2.24 0.00 42.19 3.24
1405 1438 2.416202 TGCAGTGCGTTATTGTGATCTG 59.584 45.455 11.20 0.00 0.00 2.90
1513 1546 6.656693 TCTGACCTCTGAATTCCTTTTGATTC 59.343 38.462 2.27 0.00 0.00 2.52
1514 1547 5.711976 TGACCTCTGAATTCCTTTTGATTCC 59.288 40.000 2.27 0.00 0.00 3.01
1518 1551 4.082787 TCTGAATTCCTTTTGATTCCGTGC 60.083 41.667 2.27 0.00 0.00 5.34
1525 1558 1.865788 TTTGATTCCGTGCCAGCTGC 61.866 55.000 8.66 4.57 41.77 5.25
1568 1601 5.627499 ATCAAGTGTTGCGTATGTTTGAT 57.373 34.783 0.00 0.00 0.00 2.57
1576 1609 7.003072 GTGTTGCGTATGTTTGATTGATTTTG 58.997 34.615 0.00 0.00 0.00 2.44
1579 1612 8.434661 GTTGCGTATGTTTGATTGATTTTGATT 58.565 29.630 0.00 0.00 0.00 2.57
1627 1660 0.095935 CGTTTGAGCTCCTGAATGCG 59.904 55.000 12.15 3.69 0.00 4.73
1631 1664 0.321346 TGAGCTCCTGAATGCGTTGA 59.679 50.000 12.15 0.00 0.00 3.18
1693 1726 6.067263 TGTATTTGGAGAAAAAGAACCACG 57.933 37.500 0.00 0.00 31.87 4.94
1720 1753 5.300286 AGGGATCTTGTTGTTCAAAGAACAG 59.700 40.000 11.80 2.45 42.15 3.16
1721 1754 4.978580 GGATCTTGTTGTTCAAAGAACAGC 59.021 41.667 16.51 16.51 42.15 4.40
1728 1761 2.354510 TGTTCAAAGAACAGCTTGACCG 59.645 45.455 8.39 0.00 36.80 4.79
1730 1763 3.462483 TCAAAGAACAGCTTGACCGTA 57.538 42.857 0.00 0.00 36.80 4.02
1774 1807 1.961394 CGGGGGTCTGAAATCGATCTA 59.039 52.381 0.00 0.00 0.00 1.98
1775 1808 2.364324 CGGGGGTCTGAAATCGATCTAA 59.636 50.000 0.00 0.00 0.00 2.10
1776 1809 3.181469 CGGGGGTCTGAAATCGATCTAAA 60.181 47.826 0.00 0.00 0.00 1.85
1955 1988 4.320567 GCTGGAAGAGTAAGTCTTTTTGGC 60.321 45.833 0.00 0.00 46.21 4.52
1968 2002 3.003897 TCTTTTTGGCGCGTATTTGAACT 59.996 39.130 8.43 0.00 0.00 3.01
1978 2012 5.076765 CGCGTATTTGAACTTTCGATTGAA 58.923 37.500 0.00 0.00 0.00 2.69
2154 2222 4.669206 ATGATGTCAAGCTAGAGAGTGG 57.331 45.455 0.00 0.00 0.00 4.00
2159 2227 3.243873 TGTCAAGCTAGAGAGTGGTGTTG 60.244 47.826 0.00 0.00 0.00 3.33
2161 2229 3.388024 TCAAGCTAGAGAGTGGTGTTGTT 59.612 43.478 0.00 0.00 0.00 2.83
2168 2236 2.039084 GAGAGTGGTGTTGTTCCTCCAT 59.961 50.000 0.00 0.00 32.45 3.41
2224 2292 7.283354 TGTGGTGTTCATGTTACTGTGAATTAA 59.717 33.333 6.93 0.00 36.79 1.40
2356 2424 9.131791 GATATTGAACAGGGTTATTTATGTGGT 57.868 33.333 0.00 0.00 0.00 4.16
2818 4517 2.124693 AGCTAGCGCTCAGGTCTCC 61.125 63.158 16.34 0.00 45.15 3.71
2905 4608 7.981225 CAGGTAGAAAATCAATATTGGGGTTTG 59.019 37.037 15.36 0.00 0.00 2.93
3072 4777 4.274978 GAGGGGGAGATAGTAGATGCTAC 58.725 52.174 0.00 0.00 0.00 3.58
3135 4840 7.170828 GTGAGTATCGTTTATGTCAATGCCATA 59.829 37.037 0.00 0.00 38.61 2.74
3136 4841 7.384932 TGAGTATCGTTTATGTCAATGCCATAG 59.615 37.037 0.00 0.00 38.61 2.23
3137 4842 7.441836 AGTATCGTTTATGTCAATGCCATAGA 58.558 34.615 0.00 0.00 0.00 1.98
3170 4876 2.802247 CACACATATATGTCCTGGTGCG 59.198 50.000 15.60 4.88 39.39 5.34
3173 4879 0.324943 ATATATGTCCTGGTGCGGGC 59.675 55.000 0.00 0.00 0.00 6.13
3323 5029 5.156355 GTGTAGTCAGCAACATGAATTTGG 58.844 41.667 0.00 0.00 0.00 3.28
3384 5090 3.595819 GCAGATGGTGGCAAGTCC 58.404 61.111 0.00 0.00 0.00 3.85
3664 5370 5.581605 ACAGCAGGTAATGAATAATTTGCG 58.418 37.500 0.00 0.00 35.54 4.85
3703 5409 8.792830 TGCAAGCTTACTACAGAATTTCTTAT 57.207 30.769 0.00 0.00 0.00 1.73
3841 5552 2.033151 CAGTGACATGCATGACGCTATG 60.033 50.000 33.70 23.73 40.30 2.23
3865 5576 4.623932 TTGAAGTGGCAGAGATTACACT 57.376 40.909 0.00 0.00 45.34 3.55
3954 5665 9.958180 TGATGTTCCTTTGAAATAGTTGAGATA 57.042 29.630 0.00 0.00 30.79 1.98
4036 5747 5.124457 TCCTTTTGCAATCTCAGTATTCTGC 59.876 40.000 0.00 0.00 41.10 4.26
4231 5942 4.128925 TCTGTGACAGAATCATAGTGCC 57.871 45.455 13.74 0.00 44.71 5.01
4436 6147 7.407393 ACTGTAAGGTGAATAACTCTCTACC 57.593 40.000 0.00 0.00 39.30 3.18
4509 6220 9.255304 CCTCTAATTAATAGAACTCTTCTGCAC 57.745 37.037 0.00 0.00 40.12 4.57
4552 6263 8.414003 TCCAGTTAGCTAATATAGTGTTCAGTG 58.586 37.037 9.88 0.00 0.00 3.66
4601 6312 3.081061 TGCACAATAGTGGCTTACCTTG 58.919 45.455 0.00 0.00 45.98 3.61
4610 6321 1.207593 GCTTACCTTGTGCAGCACG 59.792 57.895 20.67 9.10 37.14 5.34
4678 6389 3.415212 TGCAGGAACCAAGAAGAGATTG 58.585 45.455 0.00 0.00 0.00 2.67
4707 6418 1.131883 CTCTGCATCAAAGGCCTTTCG 59.868 52.381 28.16 21.50 0.00 3.46
4741 6452 3.428452 CCACGCGTCTAACAGATTTAGGA 60.428 47.826 9.86 0.00 0.00 2.94
4755 6466 3.616956 TTTAGGACAGCCTCAGTGATG 57.383 47.619 0.00 0.00 45.54 3.07
4809 6520 3.330267 CTCCAGTTTGAGCAGAAGGTAC 58.670 50.000 0.00 0.00 0.00 3.34
4883 6594 5.376625 TGCTACCATTGTATCTTGGATTCC 58.623 41.667 0.00 0.00 36.79 3.01
4890 6601 6.409005 CCATTGTATCTTGGATTCCAGAGACT 60.409 42.308 20.56 12.91 33.81 3.24
4967 6678 1.087501 GATTCAGGGCGTTCCTTGTC 58.912 55.000 0.00 0.00 45.47 3.18
4974 6685 3.550656 CGTTCCTTGTCGCTCCAC 58.449 61.111 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.031571 CAACATGCGCCCTGTACCAT 61.032 55.000 12.45 0.00 0.00 3.55
48 49 1.613630 GAGGGAAGCTGGTCCAGGA 60.614 63.158 20.72 0.00 39.70 3.86
159 160 2.974698 GCGTGGCTTCTGTGCTGT 60.975 61.111 0.00 0.00 0.00 4.40
247 248 1.371337 GAATCACGCATCAGGCTGCA 61.371 55.000 10.34 0.00 42.40 4.41
250 251 1.522355 CGGAATCACGCATCAGGCT 60.522 57.895 0.00 0.00 41.67 4.58
300 301 2.285602 CGGATGAGTTAAATGTTCGGCG 60.286 50.000 0.00 0.00 0.00 6.46
349 353 4.154375 TCGCGTTTAAAATAGATGCCACAA 59.846 37.500 5.77 0.00 0.00 3.33
351 355 4.033587 TCTCGCGTTTAAAATAGATGCCAC 59.966 41.667 5.77 0.00 0.00 5.01
356 360 7.360575 AGTTGTTCTCGCGTTTAAAATAGAT 57.639 32.000 5.77 0.00 0.00 1.98
365 369 4.271533 TCAAACATAGTTGTTCTCGCGTTT 59.728 37.500 5.77 0.00 45.30 3.60
366 370 3.805422 TCAAACATAGTTGTTCTCGCGTT 59.195 39.130 5.77 0.00 45.30 4.84
367 371 3.386486 TCAAACATAGTTGTTCTCGCGT 58.614 40.909 5.77 0.00 45.30 6.01
372 376 8.188139 ACGACAAAATTCAAACATAGTTGTTCT 58.812 29.630 0.00 0.00 45.30 3.01
756 760 1.403679 CATCGTCGAGGAGAGCTTCTT 59.596 52.381 13.85 0.00 0.00 2.52
760 764 1.234821 GATCATCGTCGAGGAGAGCT 58.765 55.000 15.42 0.00 0.00 4.09
763 767 1.335182 GCTTGATCATCGTCGAGGAGA 59.665 52.381 15.42 10.96 31.46 3.71
764 768 1.066152 TGCTTGATCATCGTCGAGGAG 59.934 52.381 15.42 2.83 31.46 3.69
765 769 1.066152 CTGCTTGATCATCGTCGAGGA 59.934 52.381 12.49 12.49 31.46 3.71
766 770 1.485397 CTGCTTGATCATCGTCGAGG 58.515 55.000 0.00 0.00 31.46 4.63
767 771 1.485397 CCTGCTTGATCATCGTCGAG 58.515 55.000 0.00 0.00 33.53 4.04
768 772 0.528466 GCCTGCTTGATCATCGTCGA 60.528 55.000 0.00 0.00 0.00 4.20
769 773 1.815212 CGCCTGCTTGATCATCGTCG 61.815 60.000 0.00 0.00 0.00 5.12
770 774 1.930100 CGCCTGCTTGATCATCGTC 59.070 57.895 0.00 0.00 0.00 4.20
771 775 2.176273 GCGCCTGCTTGATCATCGT 61.176 57.895 0.00 0.00 38.39 3.73
772 776 1.504647 ATGCGCCTGCTTGATCATCG 61.505 55.000 4.18 0.00 43.34 3.84
773 777 0.040336 CATGCGCCTGCTTGATCATC 60.040 55.000 4.18 0.00 46.24 2.92
774 778 2.030551 CATGCGCCTGCTTGATCAT 58.969 52.632 4.18 0.00 46.24 2.45
775 779 2.767445 GCATGCGCCTGCTTGATCA 61.767 57.895 27.46 0.00 46.24 2.92
776 780 2.025727 GCATGCGCCTGCTTGATC 59.974 61.111 27.46 0.33 46.24 2.92
777 781 1.672854 ATTGCATGCGCCTGCTTGAT 61.673 50.000 32.52 21.91 46.24 2.57
778 782 2.274232 GATTGCATGCGCCTGCTTGA 62.274 55.000 32.52 20.86 46.24 3.02
779 783 1.876714 GATTGCATGCGCCTGCTTG 60.877 57.895 32.52 12.12 46.12 4.01
780 784 2.493030 GATTGCATGCGCCTGCTT 59.507 55.556 32.52 22.19 42.75 3.91
781 785 3.524606 GGATTGCATGCGCCTGCT 61.525 61.111 32.52 17.75 42.75 4.24
782 786 3.359515 TTGGATTGCATGCGCCTGC 62.360 57.895 27.91 27.91 42.62 4.85
783 787 1.226859 CTTGGATTGCATGCGCCTG 60.227 57.895 20.32 6.63 37.32 4.85
784 788 1.378911 TCTTGGATTGCATGCGCCT 60.379 52.632 20.32 5.98 37.32 5.52
785 789 1.065273 CTCTTGGATTGCATGCGCC 59.935 57.895 14.09 14.59 37.32 6.53
786 790 1.588139 GCTCTTGGATTGCATGCGC 60.588 57.895 14.09 0.00 39.24 6.09
787 791 0.384309 ATGCTCTTGGATTGCATGCG 59.616 50.000 14.09 0.00 44.48 4.73
790 794 2.426024 GTGTCATGCTCTTGGATTGCAT 59.574 45.455 0.00 0.00 46.74 3.96
791 795 1.814394 GTGTCATGCTCTTGGATTGCA 59.186 47.619 0.00 0.00 41.13 4.08
792 796 1.133790 GGTGTCATGCTCTTGGATTGC 59.866 52.381 0.00 0.00 0.00 3.56
793 797 2.719739 AGGTGTCATGCTCTTGGATTG 58.280 47.619 0.00 0.00 0.00 2.67
794 798 3.446442 AAGGTGTCATGCTCTTGGATT 57.554 42.857 0.00 0.00 0.00 3.01
795 799 3.245016 TGAAAGGTGTCATGCTCTTGGAT 60.245 43.478 0.00 0.00 0.00 3.41
796 800 2.106338 TGAAAGGTGTCATGCTCTTGGA 59.894 45.455 0.00 0.00 0.00 3.53
797 801 2.507484 TGAAAGGTGTCATGCTCTTGG 58.493 47.619 0.00 0.00 0.00 3.61
798 802 4.022589 ACAATGAAAGGTGTCATGCTCTTG 60.023 41.667 0.00 0.00 38.28 3.02
799 803 4.147321 ACAATGAAAGGTGTCATGCTCTT 58.853 39.130 0.00 0.00 38.28 2.85
800 804 3.755378 GACAATGAAAGGTGTCATGCTCT 59.245 43.478 0.00 0.00 43.02 4.09
801 805 3.425359 CGACAATGAAAGGTGTCATGCTC 60.425 47.826 4.83 0.00 43.57 4.26
802 806 2.485426 CGACAATGAAAGGTGTCATGCT 59.515 45.455 4.83 0.00 43.57 3.79
803 807 2.855180 CGACAATGAAAGGTGTCATGC 58.145 47.619 4.83 0.00 43.57 4.06
804 808 2.226200 TGCGACAATGAAAGGTGTCATG 59.774 45.455 4.83 0.00 43.57 3.07
805 809 2.226437 GTGCGACAATGAAAGGTGTCAT 59.774 45.455 4.83 0.00 43.57 3.06
806 810 1.601903 GTGCGACAATGAAAGGTGTCA 59.398 47.619 4.83 0.00 43.57 3.58
807 811 1.069227 GGTGCGACAATGAAAGGTGTC 60.069 52.381 0.00 0.00 40.64 3.67
808 812 0.951558 GGTGCGACAATGAAAGGTGT 59.048 50.000 0.00 0.00 0.00 4.16
809 813 0.950836 TGGTGCGACAATGAAAGGTG 59.049 50.000 0.00 0.00 0.00 4.00
810 814 1.202758 TCTGGTGCGACAATGAAAGGT 60.203 47.619 0.00 0.00 0.00 3.50
811 815 1.466167 CTCTGGTGCGACAATGAAAGG 59.534 52.381 0.00 0.00 0.00 3.11
812 816 1.135859 GCTCTGGTGCGACAATGAAAG 60.136 52.381 0.00 0.00 0.00 2.62
813 817 0.874390 GCTCTGGTGCGACAATGAAA 59.126 50.000 0.00 0.00 0.00 2.69
814 818 0.035317 AGCTCTGGTGCGACAATGAA 59.965 50.000 0.00 0.00 38.13 2.57
815 819 0.390340 GAGCTCTGGTGCGACAATGA 60.390 55.000 6.43 0.00 38.13 2.57
816 820 1.364626 GGAGCTCTGGTGCGACAATG 61.365 60.000 14.64 0.00 38.13 2.82
817 821 1.078848 GGAGCTCTGGTGCGACAAT 60.079 57.895 14.64 0.00 38.13 2.71
818 822 2.343758 GGAGCTCTGGTGCGACAA 59.656 61.111 14.64 0.00 38.13 3.18
819 823 3.695606 GGGAGCTCTGGTGCGACA 61.696 66.667 14.64 0.00 38.13 4.35
820 824 2.914777 GATGGGAGCTCTGGTGCGAC 62.915 65.000 14.64 0.00 38.13 5.19
821 825 2.685017 ATGGGAGCTCTGGTGCGA 60.685 61.111 14.64 0.00 38.13 5.10
822 826 2.202987 GATGGGAGCTCTGGTGCG 60.203 66.667 14.64 0.00 38.13 5.34
823 827 0.747283 CTTGATGGGAGCTCTGGTGC 60.747 60.000 14.64 0.00 0.00 5.01
824 828 0.107312 CCTTGATGGGAGCTCTGGTG 60.107 60.000 14.64 0.00 0.00 4.17
825 829 1.919600 GCCTTGATGGGAGCTCTGGT 61.920 60.000 14.64 0.00 36.00 4.00
826 830 1.153005 GCCTTGATGGGAGCTCTGG 60.153 63.158 14.64 6.05 36.00 3.86
827 831 1.153005 GGCCTTGATGGGAGCTCTG 60.153 63.158 14.64 0.00 36.00 3.35
828 832 1.617536 TGGCCTTGATGGGAGCTCT 60.618 57.895 14.64 0.00 36.00 4.09
829 833 1.153005 CTGGCCTTGATGGGAGCTC 60.153 63.158 4.71 4.71 36.00 4.09
830 834 2.687610 CCTGGCCTTGATGGGAGCT 61.688 63.158 3.32 0.00 36.00 4.09
831 835 2.123982 CCTGGCCTTGATGGGAGC 60.124 66.667 3.32 0.00 36.00 4.70
832 836 1.225704 GTCCTGGCCTTGATGGGAG 59.774 63.158 3.32 0.00 36.00 4.30
833 837 1.541118 TGTCCTGGCCTTGATGGGA 60.541 57.895 3.32 0.00 36.00 4.37
834 838 1.379044 GTGTCCTGGCCTTGATGGG 60.379 63.158 3.32 0.00 36.00 4.00
835 839 0.962356 GTGTGTCCTGGCCTTGATGG 60.962 60.000 3.32 0.00 39.35 3.51
836 840 0.250858 TGTGTGTCCTGGCCTTGATG 60.251 55.000 3.32 0.00 0.00 3.07
837 841 0.478072 TTGTGTGTCCTGGCCTTGAT 59.522 50.000 3.32 0.00 0.00 2.57
838 842 0.257328 TTTGTGTGTCCTGGCCTTGA 59.743 50.000 3.32 0.00 0.00 3.02
839 843 1.331214 ATTTGTGTGTCCTGGCCTTG 58.669 50.000 3.32 0.00 0.00 3.61
840 844 1.963515 GAATTTGTGTGTCCTGGCCTT 59.036 47.619 3.32 0.00 0.00 4.35
841 845 1.133513 TGAATTTGTGTGTCCTGGCCT 60.134 47.619 3.32 0.00 0.00 5.19
842 846 1.327303 TGAATTTGTGTGTCCTGGCC 58.673 50.000 0.00 0.00 0.00 5.36
843 847 3.319755 CAATGAATTTGTGTGTCCTGGC 58.680 45.455 0.00 0.00 0.00 4.85
844 848 3.243805 TGCAATGAATTTGTGTGTCCTGG 60.244 43.478 0.00 0.00 37.65 4.45
845 849 3.979948 TGCAATGAATTTGTGTGTCCTG 58.020 40.909 0.00 0.00 37.65 3.86
846 850 4.669206 TTGCAATGAATTTGTGTGTCCT 57.331 36.364 0.00 0.00 37.65 3.85
847 851 5.523188 TCTTTTGCAATGAATTTGTGTGTCC 59.477 36.000 0.00 0.00 37.65 4.02
848 852 6.586868 TCTTTTGCAATGAATTTGTGTGTC 57.413 33.333 0.00 0.00 37.65 3.67
849 853 6.981762 TTCTTTTGCAATGAATTTGTGTGT 57.018 29.167 0.00 0.00 37.65 3.72
850 854 8.123575 TGATTTCTTTTGCAATGAATTTGTGTG 58.876 29.630 13.69 0.00 37.65 3.82
851 855 8.211116 TGATTTCTTTTGCAATGAATTTGTGT 57.789 26.923 13.69 1.23 37.65 3.72
857 861 9.333724 GGGAATATGATTTCTTTTGCAATGAAT 57.666 29.630 13.69 6.54 0.00 2.57
858 862 8.542080 AGGGAATATGATTTCTTTTGCAATGAA 58.458 29.630 0.00 5.62 0.00 2.57
859 863 7.982919 CAGGGAATATGATTTCTTTTGCAATGA 59.017 33.333 0.00 0.00 0.00 2.57
860 864 7.982919 TCAGGGAATATGATTTCTTTTGCAATG 59.017 33.333 0.00 0.00 0.00 2.82
861 865 8.081517 TCAGGGAATATGATTTCTTTTGCAAT 57.918 30.769 0.00 0.00 0.00 3.56
862 866 7.479352 TCAGGGAATATGATTTCTTTTGCAA 57.521 32.000 0.00 0.00 0.00 4.08
863 867 7.479352 TTCAGGGAATATGATTTCTTTTGCA 57.521 32.000 0.00 0.00 0.00 4.08
864 868 8.776376 TTTTCAGGGAATATGATTTCTTTTGC 57.224 30.769 0.00 0.00 0.00 3.68
867 871 9.387257 GCATTTTTCAGGGAATATGATTTCTTT 57.613 29.630 0.00 0.00 0.00 2.52
868 872 8.542080 TGCATTTTTCAGGGAATATGATTTCTT 58.458 29.630 0.00 0.00 0.00 2.52
869 873 8.081517 TGCATTTTTCAGGGAATATGATTTCT 57.918 30.769 0.00 0.00 0.00 2.52
870 874 8.721019 TTGCATTTTTCAGGGAATATGATTTC 57.279 30.769 0.00 0.00 0.00 2.17
871 875 9.517868 TTTTGCATTTTTCAGGGAATATGATTT 57.482 25.926 0.00 0.00 0.00 2.17
872 876 9.169592 CTTTTGCATTTTTCAGGGAATATGATT 57.830 29.630 0.00 0.00 0.00 2.57
873 877 8.323567 ACTTTTGCATTTTTCAGGGAATATGAT 58.676 29.630 0.00 0.00 0.00 2.45
874 878 7.603404 CACTTTTGCATTTTTCAGGGAATATGA 59.397 33.333 0.00 0.00 0.00 2.15
875 879 7.603404 TCACTTTTGCATTTTTCAGGGAATATG 59.397 33.333 0.00 0.00 0.00 1.78
876 880 7.678837 TCACTTTTGCATTTTTCAGGGAATAT 58.321 30.769 0.00 0.00 0.00 1.28
877 881 7.060383 TCACTTTTGCATTTTTCAGGGAATA 57.940 32.000 0.00 0.00 0.00 1.75
878 882 5.927819 TCACTTTTGCATTTTTCAGGGAAT 58.072 33.333 0.00 0.00 0.00 3.01
879 883 5.350504 TCACTTTTGCATTTTTCAGGGAA 57.649 34.783 0.00 0.00 0.00 3.97
880 884 5.070180 TGATCACTTTTGCATTTTTCAGGGA 59.930 36.000 0.00 0.00 0.00 4.20
881 885 5.299148 TGATCACTTTTGCATTTTTCAGGG 58.701 37.500 0.00 0.00 0.00 4.45
882 886 6.847956 TTGATCACTTTTGCATTTTTCAGG 57.152 33.333 0.00 0.00 0.00 3.86
883 887 7.738609 CGATTTGATCACTTTTGCATTTTTCAG 59.261 33.333 0.00 0.00 0.00 3.02
884 888 7.307278 CCGATTTGATCACTTTTGCATTTTTCA 60.307 33.333 0.00 0.00 0.00 2.69
885 889 7.011189 CCGATTTGATCACTTTTGCATTTTTC 58.989 34.615 0.00 0.00 0.00 2.29
886 890 6.482973 ACCGATTTGATCACTTTTGCATTTTT 59.517 30.769 0.00 0.00 0.00 1.94
887 891 5.990996 ACCGATTTGATCACTTTTGCATTTT 59.009 32.000 0.00 0.00 0.00 1.82
888 892 5.540911 ACCGATTTGATCACTTTTGCATTT 58.459 33.333 0.00 0.00 0.00 2.32
889 893 5.138125 ACCGATTTGATCACTTTTGCATT 57.862 34.783 0.00 0.00 0.00 3.56
890 894 4.789012 ACCGATTTGATCACTTTTGCAT 57.211 36.364 0.00 0.00 0.00 3.96
891 895 5.009110 TGTTACCGATTTGATCACTTTTGCA 59.991 36.000 0.00 0.00 0.00 4.08
892 896 5.457140 TGTTACCGATTTGATCACTTTTGC 58.543 37.500 0.00 0.00 0.00 3.68
893 897 8.519492 AAATGTTACCGATTTGATCACTTTTG 57.481 30.769 0.00 0.00 0.00 2.44
894 898 9.541143 AAAAATGTTACCGATTTGATCACTTTT 57.459 25.926 0.00 0.00 0.00 2.27
927 931 8.584157 ACAGATTTGTCATAGGTATTTTGCAAA 58.416 29.630 8.05 8.05 29.46 3.68
928 932 8.121305 ACAGATTTGTCATAGGTATTTTGCAA 57.879 30.769 0.00 0.00 29.46 4.08
964 968 3.680786 TGCCTCGGGTCGTGTCTG 61.681 66.667 0.00 0.00 0.00 3.51
1053 1063 1.613630 ACCCTCACCGGCATCTTCT 60.614 57.895 0.00 0.00 0.00 2.85
1100 1110 2.436824 GGCGAAACCTGAGGAGGC 60.437 66.667 4.99 2.19 44.33 4.70
1139 1170 2.838467 GCATGGAGATGGGAGGGGG 61.838 68.421 0.00 0.00 0.00 5.40
1140 1171 0.474466 TAGCATGGAGATGGGAGGGG 60.474 60.000 0.00 0.00 0.00 4.79
1141 1172 0.689623 GTAGCATGGAGATGGGAGGG 59.310 60.000 0.00 0.00 0.00 4.30
1142 1173 0.689623 GGTAGCATGGAGATGGGAGG 59.310 60.000 0.00 0.00 0.00 4.30
1143 1174 0.689623 GGGTAGCATGGAGATGGGAG 59.310 60.000 0.00 0.00 0.00 4.30
1144 1175 0.030195 TGGGTAGCATGGAGATGGGA 60.030 55.000 0.00 0.00 0.00 4.37
1145 1176 0.109342 GTGGGTAGCATGGAGATGGG 59.891 60.000 0.00 0.00 0.00 4.00
1146 1177 0.250038 CGTGGGTAGCATGGAGATGG 60.250 60.000 0.00 0.00 0.00 3.51
1147 1178 0.882042 GCGTGGGTAGCATGGAGATG 60.882 60.000 0.00 0.00 34.19 2.90
1148 1179 1.447643 GCGTGGGTAGCATGGAGAT 59.552 57.895 0.00 0.00 34.19 2.75
1149 1180 2.900273 GCGTGGGTAGCATGGAGA 59.100 61.111 0.00 0.00 34.19 3.71
1150 1181 2.586079 CGCGTGGGTAGCATGGAG 60.586 66.667 0.00 0.00 34.19 3.86
1151 1182 4.830765 GCGCGTGGGTAGCATGGA 62.831 66.667 8.43 0.00 34.19 3.41
1191 1222 2.828145 GGATCTGGAGCTGGGAGC 59.172 66.667 0.00 0.00 42.84 4.70
1192 1223 0.831288 ATCGGATCTGGAGCTGGGAG 60.831 60.000 0.62 0.00 0.00 4.30
1262 1293 2.777692 GTCCAATCCCAAGGGTGATCTA 59.222 50.000 4.80 0.00 36.47 1.98
1270 1301 0.179018 GATCCGGTCCAATCCCAAGG 60.179 60.000 0.00 0.00 0.00 3.61
1274 1305 1.227556 CACGATCCGGTCCAATCCC 60.228 63.158 0.00 0.00 0.00 3.85
1277 1308 2.202878 CGCACGATCCGGTCCAAT 60.203 61.111 0.00 0.00 0.00 3.16
1278 1309 3.350909 CTCGCACGATCCGGTCCAA 62.351 63.158 0.00 0.00 0.00 3.53
1289 1320 4.802039 ACAGTATACCAAATTACTCGCACG 59.198 41.667 0.00 0.00 0.00 5.34
1356 1389 2.474816 CCGAATTACAGCAGCCTACTC 58.525 52.381 0.00 0.00 0.00 2.59
1383 1416 3.073678 AGATCACAATAACGCACTGCAA 58.926 40.909 1.11 0.00 0.00 4.08
1405 1438 1.696884 GAATCATCTGGACCCTCCTCC 59.303 57.143 0.00 0.00 37.46 4.30
1427 1460 2.743928 CTGGAGCAGCCGGTTCAC 60.744 66.667 1.90 0.00 40.66 3.18
1458 1491 1.295020 TCTACCCCAAATCCCCAGTG 58.705 55.000 0.00 0.00 0.00 3.66
1518 1551 2.948315 GGAATCTTCCTTAAGCAGCTGG 59.052 50.000 17.12 0.00 44.11 4.85
1541 1574 5.734855 ACATACGCAACACTTGATTATCC 57.265 39.130 0.00 0.00 0.00 2.59
1568 1601 7.179872 TCACCACCCATGAATAATCAAAATCAA 59.820 33.333 0.00 0.00 39.49 2.57
1576 1609 5.360714 ACACATTCACCACCCATGAATAATC 59.639 40.000 0.00 0.00 43.39 1.75
1579 1612 4.015764 CACACATTCACCACCCATGAATA 58.984 43.478 0.00 0.00 43.39 1.75
1585 1618 0.548510 TGACACACATTCACCACCCA 59.451 50.000 0.00 0.00 0.00 4.51
1587 1620 0.586319 CGTGACACACATTCACCACC 59.414 55.000 6.37 0.00 40.34 4.61
1627 1660 0.657368 CCGCTTTTGACACGCTCAAC 60.657 55.000 0.00 0.00 38.70 3.18
1631 1664 3.022287 CACCGCTTTTGACACGCT 58.978 55.556 0.00 0.00 0.00 5.07
1638 1671 2.226437 ACAGTATTGAGCACCGCTTTTG 59.774 45.455 0.00 0.00 39.88 2.44
1645 1678 3.412386 ACTTGGAACAGTATTGAGCACC 58.588 45.455 0.00 0.00 42.39 5.01
1693 1726 7.174946 TGTTCTTTGAACAACAAGATCCCTATC 59.825 37.037 10.25 0.00 39.77 2.08
1708 1741 2.354821 ACGGTCAAGCTGTTCTTTGAAC 59.645 45.455 3.74 3.74 31.36 3.18
1728 1761 4.318475 GCAAAAGCGTGGACCAAATTTTAC 60.318 41.667 0.00 0.00 0.00 2.01
1730 1763 2.611751 GCAAAAGCGTGGACCAAATTTT 59.388 40.909 0.00 1.20 0.00 1.82
1789 1822 0.940126 AGGCTGCAAAGCGATAATCG 59.060 50.000 0.50 0.00 43.89 3.34
1824 1857 1.537202 AGCTGCCAAACTAGAAAAGCG 59.463 47.619 0.00 0.00 34.43 4.68
1955 1988 4.634000 TCAATCGAAAGTTCAAATACGCG 58.366 39.130 3.53 3.53 0.00 6.01
1968 2002 4.518590 TCAGCTGTTCCATTTCAATCGAAA 59.481 37.500 14.67 0.00 44.99 3.46
2010 2044 2.933260 CGGTTTTGAACAACCCTTTTGG 59.067 45.455 0.00 0.00 43.12 3.28
2154 2222 5.774498 AGAGAAAAATGGAGGAACAACAC 57.226 39.130 0.00 0.00 0.00 3.32
2159 2227 5.459536 AGCAAAGAGAAAAATGGAGGAAC 57.540 39.130 0.00 0.00 0.00 3.62
2161 2229 5.888161 GGATAGCAAAGAGAAAAATGGAGGA 59.112 40.000 0.00 0.00 0.00 3.71
2168 2236 7.687941 AATTCGAGGATAGCAAAGAGAAAAA 57.312 32.000 0.00 0.00 0.00 1.94
2356 2424 4.439057 GAACATTAAGTGCCTCCATCGTA 58.561 43.478 0.00 0.00 0.00 3.43
2597 2665 5.431179 TTAAGAAAGTCTATGGTGACCCC 57.569 43.478 0.00 0.00 37.66 4.95
2647 2717 3.340814 TTGAGAGAAATCAGTCTGCCC 57.659 47.619 0.00 0.00 0.00 5.36
2971 4674 9.226606 TCAATGAATAAAAACAGATCGTAAGGT 57.773 29.630 0.00 0.00 38.47 3.50
2996 4701 3.437049 AGCCAATAAGCGAAGTTGAAGTC 59.563 43.478 0.00 0.00 38.01 3.01
3170 4876 5.254115 AGAGTAAGTTTGGAATGTTAGCCC 58.746 41.667 0.00 0.00 0.00 5.19
3304 5010 3.499338 TCCCAAATTCATGTTGCTGACT 58.501 40.909 0.00 0.00 0.00 3.41
3384 5090 2.431057 AGGATAGTTGCTAAGGTCCACG 59.569 50.000 0.00 0.00 0.00 4.94
3488 5194 5.958955 AGCATCAGAAAATTGGAAGCTAAC 58.041 37.500 0.00 0.00 0.00 2.34
3664 5370 4.228912 AGCTTGCAATGTGTAAACTGTC 57.771 40.909 0.00 0.00 0.00 3.51
3841 5552 5.645497 AGTGTAATCTCTGCCACTTCAATTC 59.355 40.000 0.00 0.00 34.64 2.17
3865 5576 0.662619 CAAGCACAGAAAGTTCGCCA 59.337 50.000 0.00 0.00 0.00 5.69
3954 5665 4.771903 TGGCACAACCGTACATACATAAT 58.228 39.130 0.00 0.00 43.94 1.28
4205 5916 5.461407 CACTATGATTCTGTCACAGATTCCG 59.539 44.000 21.62 14.37 40.39 4.30
4231 5942 5.331876 AGTTCCTCTTCAGATAAACCTCG 57.668 43.478 0.00 0.00 0.00 4.63
4310 6021 7.962964 TGTGTGTTGTAAAATGAAACCAAAA 57.037 28.000 0.00 0.00 0.00 2.44
4372 6083 2.045045 CCAAGAGCATGCCCCGAA 60.045 61.111 15.66 0.00 0.00 4.30
4436 6147 1.221466 AACACAGTGACACGGCATCG 61.221 55.000 7.81 0.00 43.02 3.84
4509 6220 4.012374 ACTGGAAACTTATGACATGCAGG 58.988 43.478 0.00 0.00 34.25 4.85
4552 6263 8.078596 GGACAATCCTATCTGCAAAAATATGTC 58.921 37.037 0.00 0.00 32.53 3.06
4610 6321 0.520404 TTCGCTGTCTACACGTCCTC 59.480 55.000 0.00 0.00 0.00 3.71
4707 6418 0.388649 ACGCGTGGACTGAGAATGTC 60.389 55.000 12.93 0.00 0.00 3.06
4741 6452 1.277557 GGAAGTCATCACTGAGGCTGT 59.722 52.381 0.00 0.00 31.06 4.40
4828 6539 4.072131 GACAAAAGGCACATGGTAGAGAA 58.928 43.478 0.00 0.00 0.00 2.87
4883 6594 2.224018 GCTGCCCTCAAGATAGTCTCTG 60.224 54.545 0.00 0.00 33.29 3.35
4890 6601 0.326522 TCCAGGCTGCCCTCAAGATA 60.327 55.000 16.57 0.00 40.33 1.98
4967 6678 1.329292 TCGAAAACAAAGTGTGGAGCG 59.671 47.619 0.00 0.00 0.00 5.03
4974 6685 3.735746 GGCCAGAAATCGAAAACAAAGTG 59.264 43.478 0.00 0.00 0.00 3.16


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.